X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details sodium phosphate, alpha, beta methylene ATP, ADP, magnesium chloride, ribose-5-phosphate, ammonium sulfate, TrisHCl, PEG 400. Crystal was soaked in cadmium chloride in phosphate free conditions, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 115.6 α = 90
b = 115.6 β = 90
c = 107.67 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 274
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II -- 2000-01-01
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.8 30 98.0 0.136 -- -- 4.9 20019 19806 0.0 0.0 39.01
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.8 3.0 96.2 0.4 -- -- 3.4 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.8 30.0 0.0 0.0 19806 19806 1996 -- 0.2 0.2 0.2 0.273 random
RMS Deviations
Key Refinement Restraint Deviation
x_angle_deg 2.103
x_bond_d 0.018
x_improper_angle_d 2.137
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4597
Nucleic Acid Atoms 0
Heterogen Atoms 70
Solvent Atoms 47

Software

Software
Software Name Purpose
X-PLOR model building
X-PLOR refinement version: 3.1
R-AXIS data reduction
CCP4 data scaling version: (AGROVATA
ROTAVATA data scaling
TRUNCATE) data scaling
X-PLOR phasing